title: Cannabis sativa L. Leaf, Drought stress with Trichoderma hamatum, R2

city: Chuncheon-si

first: Byeong-Ryeol

last: Ryu

state: Gangwon-state

address: 1, Kangwondaehak-gil

department: Department of Bio-Health Convergence

country: South Korea

institute: Kangwon National Univsersity

data_processing:
The transcriptome analysis was conducted in the computational and server-sharing platform, Galaxy.
The generated reads were trimmed to remove adapter sequences and abnormally short reads using Cutadapt (version 4.4) with a minimum length setting of 20 and a quality cutoff of 20.
The trimmed reads were mapped using RNASTAR. (version 2.7.10b; length of the genomic sequence around annotated junctions: read length -1)
DEG analysis was conducted using DESeq2. (version 2.11.40.8)
Assembly: Cannabis sativa L. RefSeq genome (RefSeq: GCF_029168945.1)
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample.
Supplementary files format and content: tab-delimited text files include DESeq2 Normalized Count for each Sample. (Input: All samples, header=T)

organism: Cannabis sativa

source_name: Leaf

growth_protocol: The Cannabis sativa L. seeds were soaked in a 1% hydrogen peroxide soution for 12 hours. Then, they were planted in a 105-well seedling tray (42 mL per well) and grown for 14 days under controlled conditions of 25±2°C temperature and 43±7% relative humidity. After this period, the plants were transferred to large pots (8.5 L) and allowed to grow and adapt for an additional 30 days.

extract_protocol:
RNA was extracted using the RNeasy Micro Kit. (Qiagen, Hilden, Germany)
Libraries were prepared using the TruSeq standard mRNA. (Illumina Inc., San Diego, CA, USA)

treatment_protocol:
Drought stress groups were treated by stopping irrigation for 10 days before sampling.
Trichoderma hamatum HSKNU treatment group was treated directly in the soil rhizosphere with 5×10^7 onidia/kg (spore count/soil weight) 13 days before sampling.
Drought stress with Trichoderma hamatum The HSKNU treatment group consisted of a mixture of protocol 1 and protocol 2.

value: Leaf

value: Cannabis sativa L. Pink pepper

value: Drought stress with Trichoderma hamatum


title: Mouse colon, ChronicColitis4

status: Public on May 08 2024

type: SRA

city: Yongin-si

first: Seokhyun

last: Yoon

state: Gyeonggi-do

address: Dept of Electronics and Electrical Eng.,, 152 Jukjeon-ro, Suji-gu

department: Electronics and Electrical Eng.

institute: Dankook University

description: 10X genomics

library_source: transcriptomic single cell

data_processing:
CellRanger v6.1.1 was used to preprocess the sequencing reads with the genome provided by 10x genomicsTM and obtain the standard count matrix. (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tap-seperated values and matrix files

molecule: total RNA

organism: Mus musculus

source_name: colon

growth_protocol: Wild-type C57BL/6 female mice (6 weeks old) were purchased from Koatech (Pyeongtaek, Korea). All animals were maintained in a specific pathogen-free (SPF) condition on the basis of the Center for Laboratory Animal Science, Hanyang University (Ansan, Korea).

extract_protocol:
Intestinal tissues were prepared from C57BL/6 female mice after induction of the acute or chronic colitis model and homogenized for scRNA-seq analysis.
We used Chromium Next GEM Single Cell 3p RNA library v3.1. After dissociation, single cells, reagents, and a single Gel Bead containing barcoded oligonucleotides were encapsulated into nanoliter-scale GEMs (Gel Bead in emulsion) using the Next GEM Technology. We then sampled a pool of about 3,500,000 10x Barcodes to separately index each cell's transcriptome and cell surface protein by partitioning thousands of cells into nanoliter-scale Gel Beads-in-emulsion (GEMs), where all generated DNA molecules share a common 10x Barcode. - The poly(dT) primer captures poly-adenylated mRNA and barcoded, full-length cDNA is produced. Single Cell 3' GEX and feature barcode libraries were sequenced on the Illumina sequencing system. For paired-end sequencing, two reads were sequenced from both ends of the fragment. Library preparation and sequencing were conducted by Macrogen (Seoul, Korea).

treatment_protocol: DSS-induced acute or chronic colitis mouse model were generated using 6-week-old C57BL/6 female mice (Koatech, Pyeongtaek, Korea), as previously described [https://doi.org/10.3390/antiox10121954]. To estimate the induction of acute colitis, mice were supplied with 3% (w/v) dextran sodium sulfate (molecular weight: 36,000–50,000 kDa, MP Biomedicals, Santa ana, CA, USA) dissolved in drinking water given ad libitum. The DSS solutions were produced freshly per 2 days. Control mice not fed DSS were administered sterile distilled water. For the chronic colitis model, mice were treated with 3% DSS for 6 days in 3 cycles and drinking water for 5 days between cycles, as illustrated in Figures 1A. Compared to the animal's original body weight, the humane endpoint requiring euthanasia for weight loss is 20%. Weight loss cannot exceed 20% without an approved exception request.

tag: tissue

value: colon

tag: disease state

value: Chronic Colitis

tag: treatment

value: dextran sodium sulfate dissolved in drinking water


title: Cannabis sativa L. Leaf, Drought stress with Trichoderma hamatum, R1

library_source: transcriptomic

tag: genotype


title: Serum sample of emmetropic control IgG 2

type: protein

city: Shanghai

first: Xiangjia

last: Zhu

address: No.83 Fenyang Road

country: China

institute: Eye & ENT Hospital, Fudan University

description: IgG

hyb_protocol: After blocking 1h, HuProt array was incubated in 3 ml 1:1,000 diluted serum sample to capture corresponding autoantibodies to each protein spot, and followed with 1:2,000 diluted Cy3-conjugated goat anti-human IgG (Jackson, 109-165-008) and Alexa Fluor 647-affinipure donkey anti-human IgM (Jackson, 709-605-073) to fluorescently label IgG and IgM of captured autoantibodies, respectively.

scan_protocol: Scanned using the GenePix 4000B Microarray Scanner (Molecular Devices, Sunnyvale, CA, USA) and analyzed with GenePix Pro 6.0 software (Molecular Devices, Sunnyvale, CA, USA)

data_processing: The signal intensity of each protein spot was calculated as the ratio of foreground to background signal intensity. Each protein was duplicated in pairs, thus, the signal intensity of each autoantibody was calculated as the mean of both protein spots.

molecule: protein

organism: Homo sapiens

source_name: Emmetropia

extract_protocol: 1 ml venous blood per subject was collected into a promoting coagulant vacuum blood tube. The top layer serum samples after centrifugation at 3000 rpm for 10 min at 4 °C within 4 h after collection were sucked out and stored at −80 °C until use.

value: Sera

tag: molecular

value: Autoantibody

tag: age (years)

tag: Sex

value: Male

tag: al


title: Pt-02 [ATAC-seq]

city: New York

first: Franco

last: Izzo

state: NY

address: 1470 Madison Avenue

department: Oncological Sciences

country: USA

institute: Icahn School of Medicine at Mount Sinai

description: Fragment file obtained after processing of raw sequencing files through the cell-ranger-atac (v2.0.0) pipeline

library_source: genomic

data_processing:
FASTQ files were processed through the cell-ranger-atac (v2.0.0). Single cell ATAC-seq metadata files were generated by analysis with ArchR (v1.0.0),  Gotcha (v1.0.0) and GotchaMito (v1.0.0)
Assembly: hg38
Supplementary files format and content: Fragment files output from cell-ranger-atac (v2.0.0) pipeline as tab separated files. Metadata including cell cluster and genotype assignments is available as .csv files.

molecule: genomic DNA

source_name: Peripheral blood mononuclear cells (PBMC)

growth_protocol: Cell lines were cultivated in the following conditions: HEL: ; SET-2: ; CCRF-CEM: ; CA46: .

extract_protocol:
Patient samples were FACS-sorted using CD34+ DAPI- gating. Downstream processing using the 10X Chromium Solution platform for single cell ATAC sequencing, with the modifications of the GoT-ChA protocol.
Nuclei were subsequently processed according to the Chromium Next GEM Single Cell ATAC Solution user guide (version CG000209 Rev F, 10x Genomics) with the following modifications: 1- During the GEM Generation and Barcoding reaction (Step 2.1), 1 μL of 22.5 μM GoT-ChA primer mix was added to the barcoding reaction mixture. The primers used are GoT-ChA_R1N (locus-specific primer with a Read 1N handle sequence: TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG - [22bp locus specific]) and GoT-ChA_IS2 (locus- specific primer with an IS2 handle sequence: AGCAAGTGAGAAGCATCGTGTC - [22bp locus specific]). These primers allow for exponential amplification of the GoT-ChA fragments, relative to the linear amplification of ATAC fragments. 2- During the Post GEM Incubation Cleanup (Step 3.2), 45.5 μL of Elution Solution I is used to elute material from SPRIselect beads. 5 μL is used for GoT-ChA library construction, and the remaining 40 μL are used for ATAC library construction as indicated in the standard protocol. 3 - To generate the GoT-ChA library, two additional PCRs were performed on the 5 μL set aside during Step 3.2. The first PCR aims to amplify genotyping fragments prior to sample indexing and uses P5 (binds the P5 Illumina sequencing handle: AATGATACGGCGACCACCGAGATCTACAC) and GoT- ChA_nested (a nested, biotinylated, locus specific primer with a TruSeq Small RNA Read 2 handle: /5BiosG/CCTTGGCACCCGAGAATTCCA-[22bp locus specific]) primers with the following thermocycler program: 95 °C for 3 min; 15 cycles of 95 °C for 20 s, 65°C for 30 s and 72°C for 20 s; followed by 72°C for 5 min and ending with hold at 4°C. After a 1.2X SPRIselect clean up, biotinylated PCR product is bound and isolated using Dynabeads M-280 Streptavidin magnetic beads (Thermo Fisher Scientific, #11206D). Briefly, beads are washed three times with 1X sodium chloride-sodium phosphate-EDTA buffer (SSPE, VWR, #VWRV0810- 4L), added to the purified PCR product, and incubated at room temperature for 15 minutes. The beads are then washed twice with 1X SSPE buffer and once with 10 mM Tris-HCl (pH 8.0) before resuspending in water. The bead-bound fragments are then amplified and sample indexed using P5 and RPI-X (binds the TruSeq Small RNA Read 2 handle and adds a sample index and P7 Illumina sequencing handle: CAAGCAGAAGACGGCATACGAGATXXXXXXXXGTGAC TGGAGTTCCTTGGCACCCGAGAATTCCA, “X” denotes user-defined sample index) primers with the following thermocycler program: 95 °C for 3 min; 6- 10 cycles of 95 °C for 20 s, 65°C for 30 s and 72°C for 20 s; followed by 72°C for 5 min and ending with hold at 4°C
ATAC libraries were sequenced to a depth of 25,000 read pairs per nucleus and GoT-ChA libraries were sequenced to 5,000 read pairs per nucleus

tag: sample description

value: Patient 2 - Myelofibrosis untreated stage

tag: cell type

tag: mpn subtype

value: Myelofibrosis

value: Untreated


title: Cannabis sativa L. Leaf, Trichoderma hamatum treatment, R3

value: Trichoderma hamatum


title: Mouse colon, ChronicColitis3

description: 10X genomics


title: hDPSC Hypo

type: RNA

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

country: Japan

institute: Toray Industries,Inc.

description: RNA in EVs

hyb_protocol: Hybridized for 16 h at 32 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

source_name: hDPSC Hypo EVs

label_protocol: Extracted total RNA was labeled with Cy5 using the 3D-Gene miRNA labeling kit (Toray, Kamakura, Japan)

extract_protocol: RNA samples were extracted from cells using miRNesy mini kit (Qiagen).

value: human dental pulp stem cells (hDPSCs)

tag: cell compartment

value: EVs

value: hypoxic


title: Cannabis sativa L. Leaf, Drought stress with Trichoderma hamatum, R3


title: Cannabis sativa L. Leaf, Trichoderma hamatum treatment, R2


title: Pt-01 (MF-T0) [ATAC-seq]

source_name: Bone marrow

value: Patient 1 - Myelofibrosis untreated stage

value: Bone marrow


title: hDPSC Normo

description: RNA in EVs

source_name: hDPSC Normo EVs

value: normoxic


title: Pt-01 (PV) [ATAC-seq]

value: Patient 1 - Polycythemia Vera stage

value: Polycythemia Vera

value: Hydroxyurea


title: FGF18 rep1

city: Singapore

first: KAIJING

last: CHEN

address: 60 Nanyang Drive

department: school of biological science

country: Singapore

institute: Nanyang Technological University

data_processing:
Adaptors were trimmed by TrimGalore (0.6.6) (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/)
Trimmed sequence reads were mapped to hg19 in pair-end mode using bowtie2 (v2.3.5.1) with default parameters.
The resulting SAM files were converted to BAM format and filtered to exclude reads with a mapq score below 30 using samtools (v1.10).
The BAM files were sorted, and duplicate reads were removed using through Picard (https://github.com/broadinstitute/picard, v 2.27.5-4).
After removing reads mapped to chrM, chrUn, and 'random' chromosomes, BAM files from replicates were merged.
Then merged bam files were converted to BigWig files with RPKM normalization using deeptools bamCoverage (v3.4.3) for data visualization on the UCSC Genome Browser.
Peaks were called using MACS2 (v2.2.7.1) (PMID: 24743991) callpeak with the following flag parameters: --shift -100 --extsize 200 --nomodel -B --SPMR -g hs, and peaks contained in the ENCODE (v2) hg19 blacklist were removed.
Assembly: hg19
Supplementary files format and content: bigWig
Supplementary files format and content: narrowPeak files were generated using MACS v2 with default settings.

growth_protocol: CRISPR knockout and K562 wild-type cells were cultured in RPMI-1640 supplemented with 10% fetal bovine serum, and 1% penicillin-streptomycin. All cultures were maintained at 37 °C, 5% CO2 in a humidified incubator.

extract_protocol:
ATAC-seq was performed using the Diagenode ATAC-seq Kit (C01080002, Diagenode) following the manufacturer’s protocol. Briefly, 200,000 EV, S1KO, S2KO and DKO K562 cells or 50,000 drug-treated cells per sample were harvested and nuclei were isolated. Immediately following the nuclei prep, the pellet was resuspended in 50 µl tagmentation mix. The transposition reaction was carried out for 30 min at 37C. The tagmented DNA was then purified and eluted in 12 µl of DNA Elution Buffer.
Library was constructed using 10 µl of tagmented DNA and 1 µl of primer pair provided by the 24 UDI for Tagmented libraries Set I (C01011034, Diagenode)  following the manufacturer’s protocol. Libraries were amplified using 11-16 cycles on the thermocycler. The DNA fragments with target sizes ranging from 200 bp to 1000 bp were selected using AMPure XP beads (Beckman Coulter) and validated using the Agilent High Sensitivity DNA kit.

treatment_protocol: EV, S1KO, S2KO and DKO K562 cells were generated using the all-in-one CRISPR/Cas9 vector system. K562 wild-type cells were either treated with 0.1% DMSO or combined treatment of GSK343 (5 uM) and X5050 (100 uM) for 72 hr.

tag: cell line

value: knockout silencer1 region


title: Mouse colon, ChronicColitis2

description: 10X genomics

value: colon

value: Chronic Colitis

value: dextran sodium sulfate dissolved in drinking water


title: RM30 [ATAC-seq]

description: Cell line mixture experiment to determine accuracy and cell recovery of the GoT-ChA genotyping method for the TP53-R248 locus

source_name: Cell line 1:1 mixture (HEL and CA46)

value: Cell mixing experiment containing the HEL and CA46 cell lines targeting the TP53R248 locus with GoT-ChA

value: Cell line 1:1 mixture (HEL and CA46)


title: EV rep2

value: untreated


title: Cannabis sativa L. Leaf, Trichoderma hamatum treatment, R1

value: Leaf

value: Cannabis sativa L. Pink pepper

value: Trichoderma hamatum


title: Mouse colon, AcuteColitis3

description: 10X genomics

value: Acute Colitis


title: Cannabis sativa L. Leaf, Drought stress, R3

value: Drought stress


title: FGF18 rep2


title: DKO rep1

value: knockout silencer1 and 2 regions


title: SM4 [ATAC-seq]

description: Cell line mixture experiment to determine accuracy and cell recovery of the GoT-ChA genotyping method for the JAK2-V617 locus

source_name: Cell line mixture 1:1:1 (HEL, SET-2 and CCRF-CEM)

value: Cell mixing experiment containing the HEL, SET-2 and CCRF-CEM cell lines targeting the JAK2V617 locus with GoT-ChA


title: Cannabis sativa L. Leaf, Drought stress, R2


title: Mouse colon, AcuteColitis2

description: 10X genomics


title: RNAseq combined 8H rep2

data_processing:
For the RNA-seq reads of K562 EV, S1KO, S2KO and DKO, we first trimmed off adaptors by trimmomatic (0.38) using option ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36. Only those paired-end reads that remained properly paired would be then mapped to the hg19 reference GTF file using kallisto(0.44.0) with option '-b 100'. Differentially expressed genes were called using sleuth(0.29.0) with gene-level aggregation and wald test.
For the RNA-seq reads of K562 DMSO, X5050, GSK343, combined 8H, combined 24H and combined 72H, we first trimmed off adaptors by trimmomatic (0.38) using option ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36. Only those paired-end reads that remained properly paired would be then mapped to the hg19 reference GTF file using STAR (2.7.3a) with parameters ”--runThreadN 16 --outSAMtype BAM SortedByCoordinate --outReadsUnmapped Fastx --quantMode GeneCounts --readFilesCommand zcat --twopassMode Basic --outFilterType BySJout --outFilterMultimapNmax 20 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --chimSegmentMin 20 --chimJunctionOverhangMin 20 --chimOutJunctionFormat 1 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --chimSegmentReadGapMax 0 --alignSJstitchMismatchNmax 0 -1 0 0 ”. Differentially expressed genes were called using Deseq2(0.29.0) .
Genome_build: hg19
Supplementary_files_format_and_content: *.tsv : *.tsv is a plaintext file of the abundance estimates generated by Kallisto. Fields contained: 1. target_id. Transcript ID; 2. length. Transcript length; 3. eff_length. Effective length of the transcript; 4. est_counts. Estimated read counts given by the bootstrapping process of Kallisto; 5. tpm. Esmated transcript per million (TPM).
Supplementary_files_format_and_content: *.tab: *.tab is a plaintext file of the abundance estimates generated by STAR with --quantMode GeneCounts option. Fields contained: 1. gene id ; 2. counts for unstranded RNA-seq; 3. counts for the 1st read strand aligned with RNA; 4. counts for the 2nd read strand aligned with RNA.

source_name: K562 cells with combination of GSK343 and X5050 for 8h

growth_protocol: All the cells were cultured in RPMI-1640 supplemented with 10% Fetal Bovine Serum (FBS) and 1% penicillin-streptomycin. All cultures were maintained at 37 °C, 5% CO2 in a humidified incubator.

extract_protocol:
Total RNA were isolated from the cells using RNeasy Mini Kit (Qiagen) together with performing on-column DNase digestion (Qiagen). RNA concentrations were determined by Nanodrop ND1000 (Thermo Scientific).
The quality of the RNA extracted was analyzed using Agilent RNA 6000 Nano Kit (Agilent), and quantitated using Nanodrop ND1000 (Thermo Scientific). Library construction was performed using TruSeq Stranded Total RNA LT (w/ Ribo-Zero Gold) Set A (Illumina) as per protocol.

treatment_protocol: EV, S1KO, S2KO and DKO cells undergoes the CRISPR excision. The drug treated K562 cells were either treated with DMSO-72h, 5uM GSK343-72h, 100uM X5050-72h or combinational treatment (5uM GSK343+100uM X5050-72h). The time course GR treatment was done for either 8h or 24h treatment of the same concentration of GR as 72h.

value: treated with GSK343 and X5050 for 8 hours


title: EV rep1


title: Mouse colon, AcuteColitis1

description: 10X genomics


title: Cannabis sativa L. Leaf, Drought stress, R1


title: control rep2

data_processing:
These libraries are SIQHiC libraries, which encompass both human and mouse DNA.
The paired-end reads were mapped to merged hg19 and mm10 reference genome using BWA mem (0.7.17-r1188).
Subsequently, only the reads mapped to the human genome were retained for further analysis.
The mapped reads were then passed to Juicer pipeline (1.5.7) to perform chimeric reads analysis, merging, generating Hi-C matrix, loop calling using HiCCUPS, and TAD calling using Arrowhead.
Assembly: hg19
Supplementary files format and content: *_merged_nodups.txt.gz: tab-delimited text files include valid pairs for each Sample ...
Supplementary files format and content: *_30.hic: hic format files generated from Juicer and can be visualized by Juicebox

extract_protocol:
One million siRNA-treated cells and four million of drug-treated K562 cells were individually fixed and subsequently mixed with fixed mouse 3T3 cells at a ratio of 4:1. The mixed cells were then used for Hi-C experiments using Arima-HiC kit (Arima Genomics) according to the manufacturer’s protocol.
Libraries were prepared using the KAPA Hyper-Prep Kit (KAPA), according to the Arima-HiC kit protocol.

treatment_protocol: CTCF siRNA knockdown was performed using ON-TARGETplus SMARTpool Human CTCF (10664) siRNA (Dharmacon L-020165-00-0005). After 48 hr incubation, cells were harvested for Hi-C. Another Hi-C experiment was performed, where K562 cells were either treated with 0.1% DMSO or 10 uM etoposide for 72 hr.

tag: siqhic restriction_enzyme

value: Arima

value: treated with 0.1% DMSO


title: RNAseq combined 8H rep1


title: Mouse colon, Healthy3

description: 10X genomics

value: Healthy

value: sterile distilled water


title: Mouse colon, Healthy2

description: 10X genomics

value: colon


title: ETS rep1

value: treated with ETS


title: Cannabis sativa L. Leaf, Control, R3

value: Control


title: control rep1


title: ETS rep2


title: Cannabis sativa L. Leaf, Control, R1


title: RNAseq combined 24H rep2

source_name: K562 cells with combination of GSK343 and X5050 for 24h

value: treated with GSK343 and X5050 for 24 hours


title: Mouse colon, ChronicColitis1

description: 10X genomics

value: Chronic Colitis

value: dextran sodium sulfate dissolved in drinking water


title: RNAseq combined 24H rep1


title: Cannabis sativa L. Leaf, Control, R2

value: Leaf

value: Cannabis sativa L. Pink pepper


title: Mouse colon, Healthy1

description: 10X genomics


title: DKO rep2


title: Control_3

status: Public on May 07 2024

city: Vienna

first: Johannes

middle: A.

last: Schmid

address: Schwarzspanierstr. 17

department: Vascular Biology and Thrombosis Research

country: Austria

institute: Med. Univ. Wien

data_processing:
Around 36 million reads were sequenced per sample. The quality of raw reads was accessed with FastQC v0.11.8 (Anon 2015). Potential contamination with e.g vectors, ribosomal and mitochondrial sequences, or even sample mislabeling, was checked with FastQ Screen v0.13.0 (Wingett and Andrews 2018). Sequences were aligned to the mouse reference genome build GRCm38.97 using STAR v2.7.3a (Dobin et al. 2013) reporting only reads that map exactly one time to the reference genome (–outFilterMultimapNmax 1). Gene counts were performed during the alignment by adding the option –quantMode GeneCounts. Generated alignment (BAM) files were indexed with SAMtoolsv1.9 (Danecek et al. 2021). RSeQC infer_experiment.py v3.0.1 (Wang et al. 2012) was used to to “guess” how RNA-seq sequencing were configured, particularly how reads were stranded for strand-specific RNA-seq data, through comparing the “strandness of reads” with the “standness of transcripts”. This is important since it allows to know from which column to take the gene counts from STAR output ReadsPerGene.out.tab files. Provided a BAM/SAM file and reference gene model, RSeQC read_distribution.py v3.0.1 (Wang et al. 2012) will calculate how mapped reads were distributed over genome feature (like CDS exon, 5’UTR exon, 3’ UTR exon, Intron, Intergenic regions). This can be useful, for example, to check for DNA contamination by checking the reads mapped to intergenic regions. Quality of the alignment was evaluated with QualiMap v.2.2.2-dev (García-Alcalde et al. 2012). Results from the different bioinformatic tools were aggregated into a single report with MultiQC v1.7 (Ewels et al. 2016).
Differential expression analysis was performed in RStudio Server using DEseq2 (v1.28.1) and and Wald test (https://genomebiology.biomedcentral.com/articles/10.1186/s13059-014-0550-8). P−values were adjusted to obtain the false discovery rate (FDR) using the Benjamini & Hochberg method (https://rss.onlinelibrary.wiley.com/doi/10.1111/j.2517-6161.1995.tb02031.x). Reported log2 fold changes were obtained by shrinkage with lfcShrink DESeq2 default function. The DESeq2 package uses a Bayesian procedure to moderate (or “shrink”) log2 fold changes from genes with very low counts and highly variable counts.
Annotation was performed with packages biomaRt version (v2.44.4) and org.Mm.eg.db (v3.11.4).
Assembly: GRCm38.97
Supplementary files format and content: txt file containing gene counts for each sample obtained from the outupt of STAR aligner version 2.7.0e using the parameter --quantMode GeneCounts
Supplementary files format and content: tsv  file containing differential expression (DE) analysis performed using DEseq2 version 1.28.1; Entrez, baseMean, log2FoldChange, lfcSE, pvalue, padj, Symbol normalized counts for each sample
Supplementary files format and content: tsv  file containing differential expression (DE) analysis performed using DEseq2 version 1.28.1; Entrez, baseMean, log2FoldChange, lfcSE, pvalue, padj, Symbol, vst transformed counts for each sample

source_name: Aorta

growth_protocol: Mice with tamoxifen-inducible, arterial endothelial cell-specific expression of constitutive active IκB kinase 2 (caIKK2) were generated by crossing BMX-CreERT2+/- mice (MGI-ID: 5513853, (9)) with mice that express a loxP-flanked STOP cassette upstream of flag-tagged caIKK2 and EGFP (MGI-ID: 3687199, (10)).

extract_protocol:
Frozen aortas were homogenized in lysis buffer (PeqGOLD total RNA isolation Kit, Thermo Fisher Scientific, Waltham, MA, US) using a Precellys® homogenizer (VWR®, Randnor, Pennsylvania). Total RNA was isolated according to the manufacture's protocol and the RNA concentration was determined with a NanoDrop (VWR®, Vienna, Austria). The reverse transcription was performed using a RevertAid First Strand cDNA Synthesis Kit (Thermo Fisher Scientific, Waltham, MA, US). Real-time PCR analysis was performed with ~10–30 ng of cDNA in a StepOnePlusTM Real-Time PCR System (Applied Biosystems, Foster City, CA, USA). Gene expression levels were quantified using specific primers and SsoAdvanced™ Universal SYBR® Green Supermix (Bio-Rad, Hercules, CA, US).
Sequencing libraries were prepared at the Core Facility Genomics, Medical University of Vienna using the NEBNext Poly(A) mRNA MagneticIsolation Module and the NEBNext Ultra™ Directional RNA Library Prep Kitfor Illumina according to manufacturer's protocol (New EnglandBiolabs). Libraries were QC‑checked on a Bioanalyzer 2100 (Agilent) using a HighSensitivity DNA Kit for correct insert size and quantitated using QubitdsDNA HS Assay (Invitrogen). Pooled libraries had an average length of 330‑360 bp and were sequenced on a HiSeq3000/4000 instrument (Illumina) in 1x50bp sequencing mode

treatment_protocol: Tamoxifen (1 mg/20g mouse) was intraperitoneally injected at five consecutive days to control (BMX-CreERT2-+/- caIKK2 fl+/fl+) and experiment mice (BMX-CreERT2+/- caIKK2 fl/fl). Mice received standard chow and water ad libitum and were kept group-housed on a regular 12 h/12 h dark/light circle. After a recovery period of 5 days (check), aortas were carefully dissected, cleaned from perivascular adipose tissue, and snap-frozen into liquid nitrogen. Mice were housed and bred at the Medical University Vienna. Ad libitum-fed male and female mice were used in this study at ∼8-12 weeks of age.

value: Aorta

value: arterial endothelial cells

value: M

tag: age

value: 11 weeks


title: Control_2


title: Control_4

value: F

value: 12 weeks


title: Control_1


title: caIKK2EC_2


title: caIKK2EC_4


title: caIKK2EC_3


title: caIKK2EC_1


title: HL60-polyAT biol rep 1

city: Beijing

first: De-Pei

last: Liu

address: Dong Dan San Tiao 5, Dongcheng District

institute: Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences

data_processing:
The raw data reads were analyzed using ANOROAD standard pipline for RNA-seq
Assembly: GRCh37/hg19
Supplementary files format and content: Excel file include FPKM values for each sample.

source_name: Blood

extract_protocol:
Total RNAs were extracted with TRIzol™ reagent. A total of 2 μg RNA per sample was used for the construction of sequencing library.
RNA libraries for RNA-seq were prepared using VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina (Vazyme, NR604-01/02) following manufacturer's protocols.

value: Blood

value: Myeloid cell


title: HL60-polyIC biol rep 2


title: HL60-60 biol rep 1


title: HL60-60 biol rep 2


title: HL60-60rc biol rep 1


title: HL60-60rc biol rep 2


title: HL60-polyIC biol rep 1


title: HUVEC-polyAT biol rep 2

source_name: Epithelial

value: Epithelial

value: Primary endothelial cells

value: Somatic cell


title: HL60-Mock biol rep 1

value: untreated


title: HUVEC-60rc biol rep 1


title: HUVEC-60 biol rep 1


title: HUVEC-60 biol rep 2


title: HUVEC-polyAT biol rep 1


title: HL60-Mock biol rep 2


title: HUVEC-polyIC biol rep 1


title: HUVEC-Mock biol rep 2


title: HUVEC-polyIC biol rep 2


title: HUVEC-60rc biol rep 2


title: HUVEC-Mock biol rep 1


title: HL60-polyAT biol rep 2


title: MPRA from K562 (ENCLB575LQM)

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR997GVD/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR997GVD
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB575LQM
fragmentation methods: none

data_processing: See GSM*_README.txt supplementary file linked below

source_name: Homo sapiens K562 cell line genetically modified (episome) using transient transfection, 24 hours post-nucleic acid delivery time

tag: line

value: cell line

tag: biosample encode accession

tag: collection date

value: not applicable

tag: geographic location

tag: encode accession

value: female

tag: health state

value: chronic myelogenous leukemia (CML)

tag: dev stage

value: adult

value: 53 years

tag: passage number

tag: lab

value: Ryan Tewhey, JAX

tag: source

value: ATCC

tag: link

value: ENCBS984HJJ at ENCODE; https://www.encodeproject.org/ENCBS984HJJ/


title: MPRA from K562 (ENCLB440TSJ)

description:
https://www.encodeproject.org/experiments/ENCSR997GVD/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR997GVD
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB440TSJ
fragmentation methods: none

tag: Sex

value: ENCBS851CXK at ENCODE; https://www.encodeproject.org/ENCBS851CXK/


title: MPRA from K562 (ENCLB737GEC)

description:
https://www.encodeproject.org/experiments/ENCSR997GVD/
***************
biological replicate number: 5
technical replicate number: 1
description:
experiment encode accession: ENCSR997GVD
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB737GEC
fragmentation methods: none

value: ENCBS772PAY at ENCODE; https://www.encodeproject.org/ENCBS772PAY/


title: MPRA from K562 (ENCLB759DEA)

description:
https://www.encodeproject.org/experiments/ENCSR997GVD/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR997GVD
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB759DEA
fragmentation methods: none

value: ENCBS508GGH at ENCODE; https://www.encodeproject.org/ENCBS508GGH/


title: MPRA from HepG2 (ENCLB516WPB)

description:
https://www.encodeproject.org/experiments/ENCSR979TSK/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR979TSK
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB516WPB
fragmentation methods: none

source_name: Homo sapiens HepG2 cell line genetically modified (episome) using transient transfection, 24 hours post-nucleic acid delivery time

value: male

value: hepatocellular carcinoma

value: child

value: 15 years

value: ENCBS293VUM at ENCODE; https://www.encodeproject.org/ENCBS293VUM/


title: MPRA from K562 (ENCLB727WQA)

description:
https://www.encodeproject.org/experiments/ENCSR997GVD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR997GVD
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB727WQA
fragmentation methods: none

value: cell line

value: ENCBS410AKJ at ENCODE; https://www.encodeproject.org/ENCBS410AKJ/


title: MPRA from HepG2 (ENCLB736AIK)

description:
https://www.encodeproject.org/experiments/ENCSR979TSK/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR979TSK
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB736AIK
fragmentation methods: none

value: not applicable

value: ENCBS899PLT at ENCODE; https://www.encodeproject.org/ENCBS899PLT/


title: MPRA from HepG2 (ENCLB973HMB)

description:
https://www.encodeproject.org/experiments/ENCSR979TSK/
***************
biological replicate number: 5
technical replicate number: 1
description:
experiment encode accession: ENCSR979TSK
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB973HMB
fragmentation methods: none

value: ENCBS603HGY at ENCODE; https://www.encodeproject.org/ENCBS603HGY/


title: MPRA from HepG2 (ENCLB014PVC)

description:
https://www.encodeproject.org/experiments/ENCSR979TSK/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR979TSK
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB014PVC
fragmentation methods: none

value: ENCBS849OCN at ENCODE; https://www.encodeproject.org/ENCBS849OCN/


title: MPRA from K562 (ENCLB253QYN)

description:
https://www.encodeproject.org/experiments/ENCSR971PLA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR971PLA
assay title: MPRA
assembly: hg19, GRCh38
possible controls: ENCSR393KCY
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB253QYN
fragmentation methods: none

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 years

value: Ryan Tewhey, JAX

value: ENCBS963MBF at ENCODE; https://www.encodeproject.org/ENCBS963MBF/


title: MPRA from K562 (ENCLB052IOY)

description:
https://www.encodeproject.org/experiments/ENCSR971PLA/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR971PLA
assay title: MPRA
assembly: hg19, GRCh38
possible controls: ENCSR393KCY
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB052IOY
fragmentation methods: none

value: ATCC

value: ENCBS269MBE at ENCODE; https://www.encodeproject.org/ENCBS269MBE/


title: MPRA from K562 (ENCLB614HAK)

description:
https://www.encodeproject.org/experiments/ENCSR971PLA/
***************
biological replicate number: 6
technical replicate number: 1
description:
experiment encode accession: ENCSR971PLA
assay title: MPRA
assembly: hg19, GRCh38
possible controls: ENCSR393KCY
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB614HAK
fragmentation methods: none

value: ENCBS091WED at ENCODE; https://www.encodeproject.org/ENCBS091WED/


title: MPRA from K562 (ENCLB220XKB)

description:
https://www.encodeproject.org/experiments/ENCSR971BEX/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR971BEX
assay title: MPRA
encode release date: 2024-04-25
lab: Ryan Tewhey, JAX
library encode accession: ENCLB220XKB
fragmentation methods: none
instrument models: Illumina NovaSeq 6000,Illumina NextSeq 500

source_name: Homo sapiens K562 cell line genetically modified (episome) using transient transfection, 48 hours post-nucleic acid delivery time

value: ENCBS049DRW at ENCODE; https://www.encodeproject.org/ENCBS049DRW/


title: MPRA from HepG2 (ENCLB088XTI)

description:
https://www.encodeproject.org/experiments/ENCSR979TSK/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR979TSK
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB088XTI
fragmentation methods: none

value: male

value: hepatocellular carcinoma

value: child

value: 15 years

value: ENCBS565ZTW at ENCODE; https://www.encodeproject.org/ENCBS565ZTW/


title: MPRA from K562 (ENCLB359CCI)

description:
https://www.encodeproject.org/experiments/ENCSR971BEX/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR971BEX
assay title: MPRA
encode release date: 2024-04-25
lab: Ryan Tewhey, JAX
library encode accession: ENCLB359CCI
fragmentation methods: none
instrument models: Illumina NovaSeq 6000,Illumina NextSeq 500

value: cell line

value: not applicable

value: ENCBS532HNP at ENCODE; https://www.encodeproject.org/ENCBS532HNP/


title: MPRA from SK-N-SH (ENCLB687SPK)

description:
https://www.encodeproject.org/experiments/ENCSR959NUX/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR959NUX
assay title: MPRA
possible controls: ENCSR020JTL
encode release date: 2024-04-25
lab: Ryan Tewhey, JAX
library encode accession: ENCLB687SPK
fragmentation methods: none

source_name: Homo sapiens SK-N-SH cell line genetically modified (episome) using transient transfection, 24 hours post-nucleic acid delivery time

value: SK-N-SH

value: female

value: Metastatic neuroblastoma from bone marrow

value: 4 years

value: ENCBS421CGM at ENCODE; https://www.encodeproject.org/ENCBS421CGM/


title: MPRA from GM12878 (ENCLB761XNI)

description:
https://www.encodeproject.org/experiments/ENCSR918IAV/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR918IAV
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB761XNI
fragmentation methods: none

source_name: Homo sapiens GM12878 cell line genetically modified (episome) using transient transfection, 24 hours post-nucleic acid delivery time

value: unknown

value: adult

value: Ryan Tewhey, JAX

value: ATCC

value: ENCBS816IYB at ENCODE; https://www.encodeproject.org/ENCBS816IYB/


title: MPRA from K562 (ENCLB069OFM)

description:
https://www.encodeproject.org/experiments/ENCSR971PLA/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR971PLA
assay title: MPRA
assembly: hg19, GRCh38
possible controls: ENCSR393KCY
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB069OFM
fragmentation methods: none

value: chronic myelogenous leukemia (CML)

value: 53 years

value: ENCBS776TVN at ENCODE; https://www.encodeproject.org/ENCBS776TVN/


title: MPRA from K562 (ENCLB644RJY)

description:
https://www.encodeproject.org/experiments/ENCSR917SFD/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR917SFD
assay title: MPRA
assembly: hg19, GRCh38
possible controls: ENCSR889TWE
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB644RJY
fragmentation methods: none

value: ENCBS456BLZ at ENCODE; https://www.encodeproject.org/ENCBS456BLZ/


title: MPRA from GM12878 (ENCLB921LZZ)

description:
https://www.encodeproject.org/experiments/ENCSR918IAV/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR918IAV
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB921LZZ
fragmentation methods: none

value: cell line

value: ENCBS566WAE at ENCODE; https://www.encodeproject.org/ENCBS566WAE/


title: MPRA from K562 (ENCLB136LWT)

description:
https://www.encodeproject.org/experiments/ENCSR971PLA/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR971PLA
assay title: MPRA
assembly: hg19, GRCh38
possible controls: ENCSR393KCY
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB136LWT
fragmentation methods: none

value: not applicable

value: ENCBS681GDU at ENCODE; https://www.encodeproject.org/ENCBS681GDU/


title: MPRA from K562 (ENCLB632HNR)

description:
https://www.encodeproject.org/experiments/ENCSR971PLA/
***************
biological replicate number: 5
technical replicate number: 1
description:
experiment encode accession: ENCSR971PLA
assay title: MPRA
assembly: hg19, GRCh38
possible controls: ENCSR393KCY
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB632HNR
fragmentation methods: none

value: female

value: ENCBS655FXT at ENCODE; https://www.encodeproject.org/ENCBS655FXT/


title: MPRA from GM12878 (ENCLB302PAC)

description:
https://www.encodeproject.org/experiments/ENCSR918IAV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR918IAV
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB302PAC
fragmentation methods: none

value: ENCBS910TCL at ENCODE; https://www.encodeproject.org/ENCBS910TCL/


title: MPRA from GM12878 (ENCLB275HHN)

description:
https://www.encodeproject.org/experiments/ENCSR918IAV/
***************
biological replicate number: 5
technical replicate number: 1
description:
experiment encode accession: ENCSR918IAV
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB275HHN
fragmentation methods: none

value: ENCBS686IMW at ENCODE; https://www.encodeproject.org/ENCBS686IMW/


title: MPRA from GM12878 (ENCLB408RCK)

description:
https://www.encodeproject.org/experiments/ENCSR918IAV/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR918IAV
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB408RCK
fragmentation methods: none

value: unknown

value: ENCBS313AGR at ENCODE; https://www.encodeproject.org/ENCBS313AGR/


title: MPRA from K562 (ENCLB820FOG)

description:
https://www.encodeproject.org/experiments/ENCSR917SFD/
***************
biological replicate number: 5
technical replicate number: 1
description:
experiment encode accession: ENCSR917SFD
assay title: MPRA
assembly: hg19, GRCh38
possible controls: ENCSR889TWE
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB820FOG
fragmentation methods: none

value: adult

value: Ryan Tewhey, JAX

value: ENCBS976CUD at ENCODE; https://www.encodeproject.org/ENCBS976CUD/


title: MPRA from K562 (ENCLB062RBC)

description:
https://www.encodeproject.org/experiments/ENCSR909JVP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR909JVP
assay title: MPRA
possible controls: ENCSR556IED
encode release date: 2024-04-25
lab: Ryan Tewhey, JAX
library encode accession: ENCLB062RBC
fragmentation methods: none

value: chronic myelogenous leukemia (CML)

value: ATCC

value: ENCBS575AWW at ENCODE; https://www.encodeproject.org/ENCBS575AWW/


title: MPRA from K562 (ENCLB450TFJ)

description:
https://www.encodeproject.org/experiments/ENCSR917SFD/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR917SFD
assay title: MPRA
assembly: hg19, GRCh38
possible controls: ENCSR889TWE
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB450TFJ
fragmentation methods: none

value: 53 years

value: ENCBS479JVH at ENCODE; https://www.encodeproject.org/ENCBS479JVH/


title: MPRA from K562 (ENCLB506OYE)

description:
https://www.encodeproject.org/experiments/ENCSR909JVP/
***************
biological replicate number: 5
technical replicate number: 1
description:
experiment encode accession: ENCSR909JVP
assay title: MPRA
possible controls: ENCSR556IED
encode release date: 2024-04-25
lab: Ryan Tewhey, JAX
library encode accession: ENCLB506OYE
fragmentation methods: none

value: cell line

value: ENCBS567VWC at ENCODE; https://www.encodeproject.org/ENCBS567VWC/


title: MPRA from K562 (ENCLB226LZW)

description:
https://www.encodeproject.org/experiments/ENCSR917SFD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR917SFD
assay title: MPRA
assembly: hg19, GRCh38
possible controls: ENCSR889TWE
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB226LZW
fragmentation methods: none

value: not applicable

value: ENCBS372PHO at ENCODE; https://www.encodeproject.org/ENCBS372PHO/


title: MPRA from K562 (ENCLB505SQC)

description:
https://www.encodeproject.org/experiments/ENCSR917SFD/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR917SFD
assay title: MPRA
assembly: hg19, GRCh38
possible controls: ENCSR889TWE
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB505SQC
fragmentation methods: none

value: female

value: ENCBS083DGH at ENCODE; https://www.encodeproject.org/ENCBS083DGH/


title: MPRA from K562 (ENCLB282NUN)

description:
https://www.encodeproject.org/experiments/ENCSR909JVP/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR909JVP
assay title: MPRA
possible controls: ENCSR556IED
encode release date: 2024-04-25
lab: Ryan Tewhey, JAX
library encode accession: ENCLB282NUN
fragmentation methods: none

value: ENCBS241VHG at ENCODE; https://www.encodeproject.org/ENCBS241VHG/


title: MPRA from K562 (ENCLB051NMI)

description:
https://www.encodeproject.org/experiments/ENCSR909JVP/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR909JVP
assay title: MPRA
possible controls: ENCSR556IED
encode release date: 2024-04-25
lab: Ryan Tewhey, JAX
library encode accession: ENCLB051NMI
fragmentation methods: none

value: ENCBS907BIO at ENCODE; https://www.encodeproject.org/ENCBS907BIO/


title: MPRA from A549 (ENCLB517BHV)

description:
https://www.encodeproject.org/experiments/ENCSR888DPV/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR888DPV
assay title: MPRA
possible controls: ENCSR441MQR
encode release date: 2024-04-25
lab: Ryan Tewhey, JAX
library encode accession: ENCLB517BHV
fragmentation methods: none

source_name: Homo sapiens A549 cell line genetically modified (episome) using transient transfection, 24 hours post-nucleic acid delivery time

value: male

value: 58 years

value: ENCBS370VQO at ENCODE; https://www.encodeproject.org/ENCBS370VQO/


title: MPRA from A549 (ENCLB335SEK)

description:
https://www.encodeproject.org/experiments/ENCSR888DPV/
***************
biological replicate number: 5
technical replicate number: 1
description:
experiment encode accession: ENCSR888DPV
assay title: MPRA
possible controls: ENCSR441MQR
encode release date: 2024-04-25
lab: Ryan Tewhey, JAX
library encode accession: ENCLB335SEK
fragmentation methods: none

value: adult

value: Ryan Tewhey, JAX

value: ENCBS662URZ at ENCODE; https://www.encodeproject.org/ENCBS662URZ/


title: MPRA from K562 (ENCLB063GWG)

description:
https://www.encodeproject.org/experiments/ENCSR909JVP/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR909JVP
assay title: MPRA
possible controls: ENCSR556IED
encode release date: 2024-04-25
lab: Ryan Tewhey, JAX
library encode accession: ENCLB063GWG
fragmentation methods: none

value: chronic myelogenous leukemia (CML)

value: ATCC

value: ENCBS588RTN at ENCODE; https://www.encodeproject.org/ENCBS588RTN/


title: MPRA from A549 (ENCLB927KXR)

description:
https://www.encodeproject.org/experiments/ENCSR888DPV/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR888DPV
assay title: MPRA
possible controls: ENCSR441MQR
encode release date: 2024-04-25
lab: Ryan Tewhey, JAX
library encode accession: ENCLB927KXR
fragmentation methods: none

value: cell line

value: ENCBS734WVD at ENCODE; https://www.encodeproject.org/ENCBS734WVD/


title: MPRA from A549 (ENCLB434ABP)

description:
https://www.encodeproject.org/experiments/ENCSR888DPV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR888DPV
assay title: MPRA
possible controls: ENCSR441MQR
encode release date: 2024-04-25
lab: Ryan Tewhey, JAX
library encode accession: ENCLB434ABP
fragmentation methods: none

value: not applicable

value: ENCBS783EFF at ENCODE; https://www.encodeproject.org/ENCBS783EFF/


title: MPRA from SK-N-SH (ENCLB264RSM)

description:
https://www.encodeproject.org/experiments/ENCSR959NUX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR959NUX
assay title: MPRA
possible controls: ENCSR020JTL
encode release date: 2024-04-25
lab: Ryan Tewhey, JAX
library encode accession: ENCLB264RSM
fragmentation methods: none

value: SK-N-SH

value: female

value: Metastatic neuroblastoma from bone marrow

value: child

value: 4 years

value: ENCBS482TNP at ENCODE; https://www.encodeproject.org/ENCBS482TNP/


title: 24hr MVA infected ATAC-seq Bio rep 2

city: Los Alamos

first: Christina

middle: Rene

last: Steadman

state: New Mexico

address: Bikini Atoll Rd

department: Earth & Environmental Sciences Division

institute: Los Alamos National Laboratory

data_processing:
Raw reads from ATAC-seq assays were trimmed and filtered with fastp to remove Nextera adaptors and reads with repetitive sequences. Reads were also filtered to remove bases with lowquality scores (q < 15). These processed reads were aligned using bwa57 to the Chlorocebussabaeus reference genome (GCF_000409795.2_Chlorocebus_sabeus_1.1_genomic.fasta)downloaded from the NCBI genome browser. Prior to alignment, the reference fasta file wasmodified to include the sequence of the Vaccina virus (Accession No. U94848, downloadedfrom GenBank). After alignment, duplicate sequenced pairs and mitochondria read pairs weremarked and removed from analysis via samblaster. After filtering, sample alignments wereanalyzed to identify loci displaying significant enrichment of paired-end reads (peaks) usingMACS2. Input alignments were further filtered using samtools with the following samtoolsflags: -F 4 -F 256 -F 512 -F 1024 -F 2048 -q 30 and then passed to MACS2. MAC2 was called inBAMPE mode, with a min-length and max-gap setting of 100 and 150 bp, respectively, inaddition to the calling summits option.
Assembly: The Chlorocebus sabaeus reference genome (GCF_000409795.2) appended with the vaccinia virus (VACV) genome, retrieved from GenBank (U94848.1)
Supplementary files format and content: MACS2 output bedgraph file converted to bigwig format. Vaccinia virus genome subtracted.

organism: Chlorocebus sabaeus

source_name: Kidney derived cell line

growth_protocol: Cryopreserved Vero cells, derived from the kidney tissue of a normal adult African greenmonkey, were sourced from the ATCC (Cat # CCL-81). Cells were thawed, passaged, expanded,and seeded for viral infection in complete medium consisting of Dulbecco’s Modified Eagle’sMedium (DMEM) containing 4 mM L-Glutamine (ATCC, Cat # 30-2002), supplemented with10% (v/v) Fetal Bovine Serum (FBS, ATCC, Cat # 30-2020) and filter-sterilized beforeuse. Vero cells were maintained at 37°C with 5% CO2 and 95% relative humidity. Vero cellswere cryopreserved at passage #7 from the original source vial using freeze medium consistingof DMEM supplemented with 10% (v/v) FBS and 5% (v/v) dimethylsulfoxide (DMSO, ATCC,Cat # 4-X).

extract_protocol:
Cells were harvested in two biological replicates (A and B) per condition (mock-infected andMVA-infected) at each timepoint (12 hrs, 18 hrs, and 24 hrs post-infection). At each timepoint,cells were washed using 1X phosphate-buffered saline (PBS, Gibco, Cat # 10010049), detachedfor 15 min at 37°C using 1X TrypLE Express Enzyme (Gibco, Cat # 12604021), andresuspended in pre-warmed complete medium before cell counting with the Scepter 3.0Handheld Cell Counter and 60 μm Counter Sensors. At each timepoint, mock-infected andMVA-infected cell suspensions were divided and processed for Hi-C, ATAC-seq and RNA-seqtechniques
For ATAC-seq (Assay for Transposase-Accessible Chromatin by sequencing), 2x10^5 cells werecryopreserved in triplicate 1 mL aliquots using freeze medium on the day of cell harvest.Aliquots were subsequently thawed into complete medium, counted to achieve 80,000 cells persample, and processed for ATAC-seq analysis per the Active Motif ATAC-seq Kit manual (Cat# 53150) using the reagents provided in the kit. In summary, cells were washed in ice-cold 1XPBS, then lysed in ice-cold ‘ATAC Lysis Buffer’, and centrifuged for 10 min at 4°C. TagmentedDNA was prepared from the cell lysates and purified via DNA purification beads. DNA librarieswere prepared from tagmented DNA amplified via PCR using Q5 Polymerase and i7 and i5Indexed Primers under the following thermocycling conditions: 72 °C for 5 min, 98 °C for 30sec, 10 cycles of: 98 °C for 10 sec, 63 °C for 30 sec, 72 °C for 1 min, then 10 °C hold. PCRamplifiedlibraries were cleaned using magnetic DNA purification beads (provided in kit).Additional bead-based size selection was performed using AmpureXP beads (Beckman, Cat #A63880) following manufacturer's protocol to remove fragments below 150bp and above600bp. DNA libraries were then quantified using a high sensitivity Qubit dsDNA QuantificationAssay kit (Thermo Scientific, Cat# Q32851), and KAPA Library Quantification Kit (Roche, Cat# KR0405), and sequenced via the Illumina NextSeq 2000 sequencer platform in paired endmode (PE151).

treatment_protocol: Cryopreserved Vero cells were thawed at passage #8 and propagated for 2 passages prior toseeding for viral infection. At the time of seeding, a cell suspension was made in pre-warmedcomplete medium and digitally counted using the Scepter 3.0 Handheld Cell Counter and 60 μmCounter Sensors (Millipore, Cat # PHCC360KIT). Cells were seeded for viral infection atpassage #11 into replicate tissue culture flasks and multi-well plates using 5x10^6 cells per T175flask or 5x10^5 cells per well in 12-well plates. Seeded flasks and plates were incubated for 24 hrsat 37°C, yielding ~1x10^7 cells per flask and ~1x10^6 cells per well at the time of infection. Modified Vaccinia Ankara virus, strain VACV-MVA, was obtained from the ATCC (Cat # VR-1508). VACV-MVA viral stock was diluted in infection medium consisting of DMEM31supplemented with 2% (v/v) FBS. Vero cells were infected at 0 hrs using 0.4 MOI in a minimalvolume of inoculum (3 mL per flask) for 1 hr at 37°C; 17 mL infection medium was added priorto incubation for 12-24 hrs at 37°C. In parallel to the flasks, 12-well plates for ICC staining andcell imaging were also infected in parallel to the flasks at 0 hr using 0.4 MOI in 300 μL per well;then 700 μL infection medium was added prior to incubation for 12-24 hrs at 37°C.

tag: tissue

value: Kidney derived cell line

value: Vero CCL-81

tag: cell type

tag: treatment

value: 24hr MVA infected


title: 18hr MVA infected ATAC-seq Bio rep 2

tag: cell line

value: 18hr MVA infected


title: MPRA from A549 (ENCLB942IDQ)

description:
https://www.encodeproject.org/experiments/ENCSR888DPV/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR888DPV
assay title: MPRA
possible controls: ENCSR441MQR
encode release date: 2024-04-25
lab: Ryan Tewhey, JAX
library encode accession: ENCLB942IDQ
fragmentation methods: none

value: male

value: adult

tag: age

value: 58 years

value: Ryan Tewhey, JAX

value: ENCBS364YLQ at ENCODE; https://www.encodeproject.org/ENCBS364YLQ/


title: 18hr MVA infected ATAC-seq Bio rep 1


title: MPRA from SK-N-SH (ENCLB068KZU)

description:
https://www.encodeproject.org/experiments/ENCSR959NUX/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR959NUX
assay title: MPRA
possible controls: ENCSR020JTL
encode release date: 2024-04-25
lab: Ryan Tewhey, JAX
library encode accession: ENCLB068KZU
fragmentation methods: none

tag: line

value: cell line

value: not applicable

value: ATCC

value: ENCBS760ZAW at ENCODE; https://www.encodeproject.org/ENCBS760ZAW/


title: 24hr MVA infected ATAC-seq Bio rep 1


title: MPRA from HepG2 (ENCLB799IMN)

description:
https://www.encodeproject.org/experiments/ENCSR885ULM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR885ULM
assay title: MPRA
assembly: hg19
possible controls: ENCSR720LEA
encode release date: 2021-09-10
lab: Ryan Tewhey, JAX
library encode accession: ENCLB799IMN
fragmentation methods: none

source_name: Homo sapiens HepG2 cell line genetically modified (episome) using transient transfection

tag: biosample encode accession

value: hepatocellular carcinoma

value: 15 years

value: ENCBS143DML at ENCODE; https://www.encodeproject.org/ENCBS143DML/


title: 18hr Mock infected ATAC-seq Bio rep 2

value: 18hr Mock infected


title: 24hr Mock infected ATAC-seq Bio rep 1

value: Kidney derived cell line

value: 24hr Mock infected


title: 18hr Mock infected ATAC-seq Bio rep 1

value: Vero CCL-81


title: 24hr Mock infected ATAC-seq Bio rep 2


title: MPRA from HepG2 (ENCLB601MOY)

description:
https://www.encodeproject.org/experiments/ENCSR885ULM/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR885ULM
assay title: MPRA
assembly: hg19
possible controls: ENCSR720LEA
encode release date: 2021-09-10
lab: Ryan Tewhey, JAX
library encode accession: ENCLB601MOY
fragmentation methods: none

tag: collection date

value: child

value: ENCBS218HKH at ENCODE; https://www.encodeproject.org/ENCBS218HKH/


title: MPRA from HepG2 (ENCLB322JGD)

description:
https://www.encodeproject.org/experiments/ENCSR885ULM/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR885ULM
assay title: MPRA
assembly: hg19
possible controls: ENCSR720LEA
encode release date: 2021-09-10
lab: Ryan Tewhey, JAX
library encode accession: ENCLB322JGD
fragmentation methods: none

tag: geographic location

value: male

value: ENCBS089AMQ at ENCODE; https://www.encodeproject.org/ENCBS089AMQ/


title: 12hr Mock infected ATAC-seq Bio rep 1

value: 12hr Mock infected


title: 12hr Mock infected ATAC-seq  Bio rep 2


title: Time Point_0dpc_Group_12dv_Sample3

city: Bellaterra

first: Jordi

last: Argilaguet Marqués

state: Barcelona

address: CAMPUS UAB EDIF.CRESA

country: Spain

institute: IRTA-CReSA

data_processing:
Reads mapped with STAR v2.7.8a
Genes quantified with RSEM v1.3.0
Assembly: Concatenation of Sscrofa11.1 and KP055815
Supplementary files format and content: Tab-delimited text file with raw counts for each sample

organism: Sus scrofa domesticus

source_name: Whole Blood

extract_protocol:
Phenol-chloroform method, and further purified using RNeasy mini Kit, QIAGEN (RNAse-free water) following the manufacturer’s protocol. DNase I (RNase-Free DNase Set, Qiagen) treatment for 15 min at room temperature was performed to ensure RNA quality. Total RNA from whole blood was submitted for sequencing to the Centre Nacional d'Anàlisi Genòmica (CNAG), Barcelona, Spain. Total RNA was quantified by Qubit RNA BR Assay kit (Thermo Fisher Scientific) and the RNA integrity was estimated by using RNA 6000 Nano Bioanalyzer 2100 Assay (Agilent).
The RNASeq libraries were prepared with KAPA mRNA HyperPrep Kit (Roche) following the manufacturer´s recommendations starting with 500 ng of total RNA as the input material. The library was quality controlled on an Agilent 2100 Bioanalyzer with the DNA 7500 assay. The libraries were sequenced on NovaSeq 6000 (Illumina) with a read length of 2x51bp, following the manufacturer’s protocol for dual indexing. Image analysis, base calling and quality scoring of the run were processed using the manufacturer’s software Real Time Analysis (RTA 3.4.4).

treatment_protocol: Whole blood was kept at -80˚C in TRIzol Reagent (Invitrogen) until use.

value: 27 weeks old

tag: diet

value: ad libitum

value: Whole Blood

value: primary

value: Peripheral Blood Mononuclear Cells (PBMCs)

tag: time

value: 0 days post-challenge

value: Vaccination


title: 12hr MVA infected ATAC-seq  Bio rep 2

value: 12hr MVA infected


title: MPRA from HepG2 (ENCLB072XKC)

description:
https://www.encodeproject.org/experiments/ENCSR885ULM/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR885ULM
assay title: MPRA
assembly: hg19
possible controls: ENCSR720LEA
encode release date: 2021-09-10
lab: Ryan Tewhey, JAX
library encode accession: ENCLB072XKC
fragmentation methods: none

value: cell line

value: not applicable

tag: encode accession

tag: health state

value: hepatocellular carcinoma

tag: dev stage

value: 15 years

value: Ryan Tewhey, JAX

value: ATCC

value: ENCBS571AZO at ENCODE; https://www.encodeproject.org/ENCBS571AZO/


title: MPRA from HCT116 (ENCLB879XSI)

description:
https://www.encodeproject.org/experiments/ENCSR873QHK/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR873QHK
assay title: MPRA
assembly: hg19, GRCh38
possible controls: ENCSR691FFI
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB879XSI
fragmentation methods: none

source_name: Homo sapiens HCT116 cell line genetically modified (episome) using transient transfection, 24 hours post-nucleic acid delivery time

value: male

value: colorectal carcinoma

value: adult

value: 48 years

tag: passage number

tag: lab

tag: source

value: ENCBS954OPO at ENCODE; https://www.encodeproject.org/ENCBS954OPO/


title: MPRA from HCT116 (ENCLB440XSH)

description:
https://www.encodeproject.org/experiments/ENCSR873QHK/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR873QHK
assay title: MPRA
assembly: hg19, GRCh38
possible controls: ENCSR691FFI
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB440XSH
fragmentation methods: none

tag: Sex

tag: link

value: ENCBS147HHZ at ENCODE; https://www.encodeproject.org/ENCBS147HHZ/


title: MPRA from HCT116 (ENCLB925HMS)

description:
https://www.encodeproject.org/experiments/ENCSR873QHK/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR873QHK
assay title: MPRA
assembly: hg19, GRCh38
possible controls: ENCSR691FFI
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB925HMS
fragmentation methods: none

value: ENCBS726KSS at ENCODE; https://www.encodeproject.org/ENCBS726KSS/


title: MPRA from HCT116 (ENCLB748HOO)

description:
https://www.encodeproject.org/experiments/ENCSR873QHK/
***************
biological replicate number: 5
technical replicate number: 1
description:
experiment encode accession: ENCSR873QHK
assay title: MPRA
assembly: hg19, GRCh38
possible controls: ENCSR691FFI
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB748HOO
fragmentation methods: none

value: ENCBS345PKA at ENCODE; https://www.encodeproject.org/ENCBS345PKA/


title: MPRA from HCT116 (ENCLB357TNR)

description:
https://www.encodeproject.org/experiments/ENCSR873QHK/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR873QHK
assay title: MPRA
assembly: hg19, GRCh38
possible controls: ENCSR691FFI
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB357TNR
fragmentation methods: none

value: ENCBS146GKH at ENCODE; https://www.encodeproject.org/ENCBS146GKH/


title: 12hr MVA infected ATAC-seq  Bio rep 1

tag: tissue

value: Kidney derived cell line

value: Vero CCL-81

tag: cell type

tag: treatment

value: 12hr MVA infected


title: MPRA from K562 (ENCLB869ECF)

description:
https://www.encodeproject.org/experiments/ENCSR857JFG/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR857JFG
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB869ECF
fragmentation methods: none

tag: line

value: cell line

value: not applicable

value: female

value: chronic myelogenous leukemia (CML)

tag: age

value: 53 years

value: ENCBS913PZR at ENCODE; https://www.encodeproject.org/ENCBS913PZR/


title: MPRA from K562 (ENCLB734JEU)

description:
https://www.encodeproject.org/experiments/ENCSR857JFG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR857JFG
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB734JEU
fragmentation methods: none

tag: biosample encode accession

tag: collection date

value: Ryan Tewhey, JAX

value: ATCC

value: ENCBS959MGG at ENCODE; https://www.encodeproject.org/ENCBS959MGG/


title: MPRA from K562 (ENCLB825FHO)

description:
https://www.encodeproject.org/experiments/ENCSR857JFG/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR857JFG
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB825FHO
fragmentation methods: none

tag: geographic location

value: adult

value: ENCBS602VJW at ENCODE; https://www.encodeproject.org/ENCBS602VJW/


title: MPRA from SK-N-SH (ENCLB154POJ)

description:
https://www.encodeproject.org/experiments/ENCSR856SQG/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR856SQG
assay title: MPRA
possible controls: ENCSR441MQR
encode release date: 2024-04-25
lab: Ryan Tewhey, JAX
library encode accession: ENCLB154POJ
fragmentation methods: none

value: SK-N-SH

value: Metastatic neuroblastoma from bone marrow

value: child

value: 4 years

value: ENCBS286VVH at ENCODE; https://www.encodeproject.org/ENCBS286VVH/


title: MPRA from K562 (ENCLB701WNN)

description:
https://www.encodeproject.org/experiments/ENCSR857JFG/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR857JFG
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB701WNN
fragmentation methods: none

value: ENCBS536CWA at ENCODE; https://www.encodeproject.org/ENCBS536CWA/


title: MPRA from SK-N-SH (ENCLB970PGB)

description:
https://www.encodeproject.org/experiments/ENCSR856SQG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR856SQG
assay title: MPRA
possible controls: ENCSR441MQR
encode release date: 2024-04-25
lab: Ryan Tewhey, JAX
library encode accession: ENCLB970PGB
fragmentation methods: none

value: cell line

value: ENCBS773MKN at ENCODE; https://www.encodeproject.org/ENCBS773MKN/


title: MPRA from SK-N-SH (ENCLB528UCL)

description:
https://www.encodeproject.org/experiments/ENCSR856SQG/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR856SQG
assay title: MPRA
possible controls: ENCSR441MQR
encode release date: 2024-04-25
lab: Ryan Tewhey, JAX
library encode accession: ENCLB528UCL
fragmentation methods: none

value: not applicable

value: female

value: ENCBS980GDO at ENCODE; https://www.encodeproject.org/ENCBS980GDO/


title: MPRA from HepG2 (ENCLB630VKR)

description:
https://www.encodeproject.org/experiments/ENCSR847SNQ/
***************
biological replicate number: 5
technical replicate number: 1
description:
experiment encode accession: ENCSR847SNQ
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB630VKR
fragmentation methods: none

value: male

value: hepatocellular carcinoma

value: 15 years

value: ENCBS459ZIF at ENCODE; https://www.encodeproject.org/ENCBS459ZIF/


title: MPRA from SK-N-SH (ENCLB666DCX)

description:
https://www.encodeproject.org/experiments/ENCSR856SQG/
***************
biological replicate number: 5
technical replicate number: 1
description:
experiment encode accession: ENCSR856SQG
assay title: MPRA
possible controls: ENCSR441MQR
encode release date: 2024-04-25
lab: Ryan Tewhey, JAX
library encode accession: ENCLB666DCX
fragmentation methods: none

value: Ryan Tewhey, JAX

value: ATCC

value: ENCBS109WAF at ENCODE; https://www.encodeproject.org/ENCBS109WAF/


title: MPRA from HepG2 (ENCLB879YAS)

description:
https://www.encodeproject.org/experiments/ENCSR847SNQ/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR847SNQ
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB879YAS
fragmentation methods: none

value: ENCBS282PZW at ENCODE; https://www.encodeproject.org/ENCBS282PZW/


title: MPRA from HepG2 (ENCLB461KCV)

description:
https://www.encodeproject.org/experiments/ENCSR847SNQ/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR847SNQ
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB461KCV
fragmentation methods: none

value: child

value: ENCBS927GQH at ENCODE; https://www.encodeproject.org/ENCBS927GQH/


title: MPRA from HepG2 (ENCLB585DAX)

description:
https://www.encodeproject.org/experiments/ENCSR847SNQ/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR847SNQ
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB585DAX
fragmentation methods: none

value: ENCBS805QCG at ENCODE; https://www.encodeproject.org/ENCBS805QCG/


title: MPRA from HepG2 (ENCLB956ZSD)

description:
https://www.encodeproject.org/experiments/ENCSR847SNQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR847SNQ
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB956ZSD
fragmentation methods: none

value: ENCBS304PDF at ENCODE; https://www.encodeproject.org/ENCBS304PDF/


title: MPRA from HepG2 (ENCLB593LSZ)

description:
https://www.encodeproject.org/experiments/ENCSR843APF/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR843APF
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB593LSZ
fragmentation methods: none

value: cell line

value: ENCBS343UGA at ENCODE; https://www.encodeproject.org/ENCBS343UGA/


title: MPRA from HepG2 (ENCLB766JWC)

description:
https://www.encodeproject.org/experiments/ENCSR843APF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR843APF
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB766JWC
fragmentation methods: none

value: not applicable

value: ENCBS548HZQ at ENCODE; https://www.encodeproject.org/ENCBS548HZQ/


title: MPRA from HepG2 (ENCLB605TKV)

description:
https://www.encodeproject.org/experiments/ENCSR843APF/
***************
biological replicate number: 5
technical replicate number: 1
description:
experiment encode accession: ENCSR843APF
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB605TKV
fragmentation methods: none

value: ENCBS156PBP at ENCODE; https://www.encodeproject.org/ENCBS156PBP/


title: MPRA from HepG2 (ENCLB405HYY)

description:
https://www.encodeproject.org/experiments/ENCSR843APF/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR843APF
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB405HYY
fragmentation methods: none

value: male

value: ENCBS058VZA at ENCODE; https://www.encodeproject.org/ENCBS058VZA/


title: MPRA from SK-N-SH (ENCLB215HLL)

description:
https://www.encodeproject.org/experiments/ENCSR833GXJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR833GXJ
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB215HLL
fragmentation methods: none

value: SK-N-SH

value: female

value: Metastatic neuroblastoma from bone marrow

value: 4 years

value: ENCBS155KVQ at ENCODE; https://www.encodeproject.org/ENCBS155KVQ/


title: MPRA from K562 (ENCLB822WFU)

description:
https://www.encodeproject.org/experiments/ENCSR857JFG/
***************
biological replicate number: 5
technical replicate number: 1
description:
experiment encode accession: ENCSR857JFG
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB822WFU
fragmentation methods: none

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 years

value: Ryan Tewhey, JAX

value: ATCC

value: ENCBS261KXF at ENCODE; https://www.encodeproject.org/ENCBS261KXF/


title: MPRA from SK-N-SH (ENCLB348NEH)

description:
https://www.encodeproject.org/experiments/ENCSR833GXJ/
***************
biological replicate number: 5
technical replicate number: 1
description:
experiment encode accession: ENCSR833GXJ
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB348NEH
fragmentation methods: none

value: cell line

value: child

value: ENCBS335JZP at ENCODE; https://www.encodeproject.org/ENCBS335JZP/


title: MPRA from SK-N-SH (ENCLB127FBU)

description:
https://www.encodeproject.org/experiments/ENCSR833GXJ/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR833GXJ
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB127FBU
fragmentation methods: none

value: not applicable

value: ENCBS346QQU at ENCODE; https://www.encodeproject.org/ENCBS346QQU/


title: MPRA from SK-N-SH (ENCLB064PTH)

description:
https://www.encodeproject.org/experiments/ENCSR833GXJ/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR833GXJ
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB064PTH
fragmentation methods: none

value: ENCBS459PON at ENCODE; https://www.encodeproject.org/ENCBS459PON/


title: MPRA from HepG2 (ENCLB090NFX)

description:
https://www.encodeproject.org/experiments/ENCSR833BYO/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR833BYO
assay title: MPRA
assembly: hg19, GRCh38
possible controls: ENCSR691FFI
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB090NFX
fragmentation methods: none

value: male

value: hepatocellular carcinoma

value: 15 years

value: ENCBS148KBN at ENCODE; https://www.encodeproject.org/ENCBS148KBN/


title: MPRA from HepG2 (ENCLB213RJY)

description:
https://www.encodeproject.org/experiments/ENCSR833BYO/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR833BYO
assay title: MPRA
assembly: hg19, GRCh38
possible controls: ENCSR691FFI
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB213RJY
fragmentation methods: none

value: ENCBS684IVJ at ENCODE; https://www.encodeproject.org/ENCBS684IVJ/


title: MPRA from K562 (ENCLB779ZOC)

description:
https://www.encodeproject.org/experiments/ENCSR820RPI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR820RPI
assay title: MPRA
possible controls: ENCSR645FSB
encode release date: 2024-04-25
lab: Ryan Tewhey, JAX
library encode accession: ENCLB779ZOC
fragmentation methods: none

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS392GHT at ENCODE; https://www.encodeproject.org/ENCBS392GHT/


title: MPRA from HepG2 (ENCLB942WCU)

description:
https://www.encodeproject.org/experiments/ENCSR833BYO/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR833BYO
assay title: MPRA
assembly: hg19, GRCh38
possible controls: ENCSR691FFI
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB942WCU
fragmentation methods: none

value: Ryan Tewhey, JAX

value: ENCBS689NPA at ENCODE; https://www.encodeproject.org/ENCBS689NPA/


title: MPRA from HepG2 (ENCLB125YBL)

description:
https://www.encodeproject.org/experiments/ENCSR833BYO/
***************
biological replicate number: 5
technical replicate number: 1
description:
experiment encode accession: ENCSR833BYO
assay title: MPRA
assembly: hg19, GRCh38
possible controls: ENCSR691FFI
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB125YBL
fragmentation methods: none

value: ATCC

value: ENCBS276KSX at ENCODE; https://www.encodeproject.org/ENCBS276KSX/


title: MPRA from HepG2 (ENCLB455YYX)

description:
https://www.encodeproject.org/experiments/ENCSR833BYO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR833BYO
assay title: MPRA
assembly: hg19, GRCh38
possible controls: ENCSR691FFI
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB455YYX
fragmentation methods: none

value: cell line

value: child

value: ENCBS979CMC at ENCODE; https://www.encodeproject.org/ENCBS979CMC/


title: MPRA from K562 (ENCLB813QPL)

description:
https://www.encodeproject.org/experiments/ENCSR820RPI/
***************
biological replicate number: 5
technical replicate number: 1
description:
experiment encode accession: ENCSR820RPI
assay title: MPRA
possible controls: ENCSR645FSB
encode release date: 2024-04-25
lab: Ryan Tewhey, JAX
library encode accession: ENCLB813QPL
fragmentation methods: none

value: not applicable

value: adult

value: 53 years

value: ENCBS054TFA at ENCODE; https://www.encodeproject.org/ENCBS054TFA/


title: MPRA from K562 (ENCLB798WYX)

description:
https://www.encodeproject.org/experiments/ENCSR820RPI/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR820RPI
assay title: MPRA
possible controls: ENCSR645FSB
encode release date: 2024-04-25
lab: Ryan Tewhey, JAX
library encode accession: ENCLB798WYX
fragmentation methods: none

value: ENCBS613ACM at ENCODE; https://www.encodeproject.org/ENCBS613ACM/


title: MPRA from K562 (ENCLB243LPN)

description:
https://www.encodeproject.org/experiments/ENCSR820RPI/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR820RPI
assay title: MPRA
possible controls: ENCSR645FSB
encode release date: 2024-04-25
lab: Ryan Tewhey, JAX
library encode accession: ENCLB243LPN
fragmentation methods: none

value: ENCBS386WLT at ENCODE; https://www.encodeproject.org/ENCBS386WLT/


title: MPRA from SK-N-SH (ENCLB778WWU)

description:
https://www.encodeproject.org/experiments/ENCSR856SQG/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR856SQG
assay title: MPRA
possible controls: ENCSR441MQR
encode release date: 2024-04-25
lab: Ryan Tewhey, JAX
library encode accession: ENCLB778WWU
fragmentation methods: none

value: SK-N-SH

value: Metastatic neuroblastoma from bone marrow

value: 4 years

value: ENCBS500YFU at ENCODE; https://www.encodeproject.org/ENCBS500YFU/


title: MPRA from GM12878 (ENCLB895RYP)

description:
https://www.encodeproject.org/experiments/ENCSR812PWW/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR812PWW
assay title: MPRA
assembly: hg19
possible controls: ENCSR720LEA
encode release date: 2021-09-10
lab: Ryan Tewhey, JAX
library encode accession: ENCLB895RYP
fragmentation methods: none

source_name: Homo sapiens GM12878 cell line genetically modified (episome) using transient transfection

value: female

value: unknown

value: Ryan Tewhey, JAX

value: ENCBS837JGR at ENCODE; https://www.encodeproject.org/ENCBS837JGR/


title: MPRA from GM12878 (ENCLB900UGU)

description:
https://www.encodeproject.org/experiments/ENCSR812PWW/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR812PWW
assay title: MPRA
assembly: hg19
possible controls: ENCSR720LEA
encode release date: 2021-09-10
lab: Ryan Tewhey, JAX
library encode accession: ENCLB900UGU
fragmentation methods: none

value: cell line

value: ATCC

value: ENCBS867IVG at ENCODE; https://www.encodeproject.org/ENCBS867IVG/


title: MPRA from GM12878 (ENCLB472UXV)

description:
https://www.encodeproject.org/experiments/ENCSR812PWW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR812PWW
assay title: MPRA
assembly: hg19
possible controls: ENCSR720LEA
encode release date: 2021-09-10
lab: Ryan Tewhey, JAX
library encode accession: ENCLB472UXV
fragmentation methods: none

value: not applicable

value: ENCBS359CKI at ENCODE; https://www.encodeproject.org/ENCBS359CKI/


title: MPRA from SK-N-SH (ENCLB504IOG)

description:
https://www.encodeproject.org/experiments/ENCSR833GXJ/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR833GXJ
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB504IOG
fragmentation methods: none

value: child

value: ENCBS704DFX at ENCODE; https://www.encodeproject.org/ENCBS704DFX/


title: Brain, Paxton benthic, female social control, trial 91

city: University Park

first: Jason

last: Keagy

state: PA

address: 410 Forest Resources Bldg

department: Ecosystem Science and Management

institute: Penn State University

data_processing:
Bioinformatic analyses were carried out using the computational resources of the Texas Advanced Computing Center (TACC).
Reads from all eight lanes were combined for each uniquely barcoded individual, separately for forward and reverse reads.
We conducted quality control checks using fastqc (v0.11.1).
We then ran Trimmomatic (v0.33)to remove a small amount of adapter contamination.
Next, reads were aligned to the Gasterosteus aculeatus Ensembl BROAD S1 draft genome (version 78) using bwa (v0.7.7).
Samtools (v1.2) was used to convert sam to bam files, and then sort and index them.
These sorted and indexed bam files were then passed to bedtools (v2.23.0) to count gene transcripts.
Assembly: Gasterosteus aculeatus Ensembl BROAD S1 draft genome (version 78)
Supplementary files format and content: Tab deliminated text file containing raw ead counts with samples in columns and genes in rows.

molecule: polyA RNA

organism: Gasterosteus aculeatus

source_name: whole brain

extract_protocol:
After 20 min of time with the courting male/ female social control or spawning (whichever came first), the female subject was killed by rapid cervical dissection, and the brain was immediately dissected under a microscope in a Sylgaard 184-lined petri-dish filled with a Ringer’s solution. Brains were stored overnight in RNAlater at 4°C and then transferred to -20°C until RNA extraction. Brains were shipped on dry ice from Michigan State University to The University of Texas at Austin where RNA was extracted using the Maxwell 16 LEV simplyRNA Tissue Kit, which utilizes a robot to increase consistency.
At the UT Austin Genomic Sequencing and Analysis Facility (GSAF) each sample (all with RIN > 7.8, 8.8 ± 0.4 mean ± SD, 11 samples do not have RIN scores) was prepared for RNA-seq using PolyA mRNA capture and given a unique barcode. A single library of all multiplexed samples was sequenced across eight lanes of an Illumina Hiseq 2500 with 2x50 PE chemistry.

value: whole brain

tag: population

value: Paxton benthic

value: female social control


title: MPRA from HepG2 (ENCLB133MDI)

description:
https://www.encodeproject.org/experiments/ENCSR843APF/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR843APF
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB133MDI
fragmentation methods: none

tag: encode accession

value: male

value: hepatocellular carcinoma

value: 15 years

value: ENCBS453UWP at ENCODE; https://www.encodeproject.org/ENCBS453UWP/


title: MPRA from HepG2 (ENCLB247OSL)

description:
https://www.encodeproject.org/experiments/ENCSR811QES/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR811QES
assay title: MPRA
possible controls: ENCSR441MQR
encode release date: 2024-04-25
lab: Ryan Tewhey, JAX
library encode accession: ENCLB247OSL
fragmentation methods: none
instrument models: Illumina NovaSeq 6000,Illumina NextSeq 500

tag: health state

value: ENCBS247VJV at ENCODE; https://www.encodeproject.org/ENCBS247VJV/


title: Brain, Paxton benthic, heterospecific courtship, trial 90

value: female

value: heterospecific courtship


title: MPRA from HepG2 (ENCLB502RRC)

description:
https://www.encodeproject.org/experiments/ENCSR811QES/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR811QES
assay title: MPRA
possible controls: ENCSR441MQR
encode release date: 2024-04-25
lab: Ryan Tewhey, JAX
library encode accession: ENCLB502RRC
fragmentation methods: none
instrument models: Illumina NovaSeq 6000,Illumina NextSeq 500

value: cell line

tag: dev stage

value: Ryan Tewhey, JAX

value: ENCBS748XLY at ENCODE; https://www.encodeproject.org/ENCBS748XLY/


title: Brain, Paxton benthic, conspecific courtship, trial 89

value: conspecific courtship


title: MPRA from A549 (ENCLB400USZ)

description:
https://www.encodeproject.org/experiments/ENCSR793OLW/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR793OLW
assay title: MPRA
assembly: hg19, GRCh38
possible controls: ENCSR437KIU
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB400USZ
fragmentation methods: none

value: not applicable

value: adult

value: 58 years

tag: passage number

value: ATCC

value: ENCBS559CLP at ENCODE; https://www.encodeproject.org/ENCBS559CLP/


title: Brain, Paxton benthic, heterospecific courtship, trial 85

value: whole brain

value: Paxton benthic


title: MPRA from A549 (ENCLB505EHQ)

description:
https://www.encodeproject.org/experiments/ENCSR793OLW/
***************
biological replicate number: 5
technical replicate number: 1
description:
experiment encode accession: ENCSR793OLW
assay title: MPRA
assembly: hg19, GRCh38
possible controls: ENCSR437KIU
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB505EHQ
fragmentation methods: none

value: male

tag: lab

value: ENCBS662BAP at ENCODE; https://www.encodeproject.org/ENCBS662BAP/


title: MPRA from A549 (ENCLB932GLQ)

description:
https://www.encodeproject.org/experiments/ENCSR793OLW/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR793OLW
assay title: MPRA
assembly: hg19, GRCh38
possible controls: ENCSR437KIU
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB932GLQ
fragmentation methods: none

tag: source

value: ENCBS451IEM at ENCODE; https://www.encodeproject.org/ENCBS451IEM/


title: Brain, Paxton benthic, female social control, trial 84

tag: Sex

value: female social control


title: MPRA from K562 (ENCLB798NYH)

description:
https://www.encodeproject.org/experiments/ENCSR820RPI/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR820RPI
assay title: MPRA
possible controls: ENCSR645FSB
encode release date: 2024-04-25
lab: Ryan Tewhey, JAX
library encode accession: ENCLB798NYH
fragmentation methods: none

value: female

value: chronic myelogenous leukemia (CML)

value: 53 years

tag: link

value: ENCBS983KLN at ENCODE; https://www.encodeproject.org/ENCBS983KLN/


title: MPRA from A549 (ENCLB558HLE)

description:
https://www.encodeproject.org/experiments/ENCSR793OLW/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR793OLW
assay title: MPRA
assembly: hg19, GRCh38
possible controls: ENCSR437KIU
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB558HLE
fragmentation methods: none

value: cell line

value: Ryan Tewhey, JAX

value: ENCBS338HAQ at ENCODE; https://www.encodeproject.org/ENCBS338HAQ/


title: Brain, Paxton benthic, conspecific courtship, trial 83

tag: tissue

value: conspecific courtship


title: Brain, Paxton limnetic, female social control, trial 79

value: Paxton limnetic


title: MPRA from A549 (ENCLB674OHT)

description:
https://www.encodeproject.org/experiments/ENCSR793OLW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR793OLW
assay title: MPRA
assembly: hg19, GRCh38
possible controls: ENCSR437KIU
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB674OHT
fragmentation methods: none

value: not applicable

value: adult

value: 58 years

value: ATCC

value: ENCBS711TEP at ENCODE; https://www.encodeproject.org/ENCBS711TEP/


title: MPRA from HEK293 (ENCLB004RPQ)

description:
https://www.encodeproject.org/experiments/ENCSR781PSG/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR781PSG
assay title: MPRA
assembly: hg19
possible controls: ENCSR701FXI
encode release date: 2021-09-10
lab: Ryan Tewhey, JAX
library encode accession: ENCLB004RPQ
fragmentation methods: none

source_name: Homo sapiens HEK293 cell line genetically modified (episome) using transient transfection

value: unknown

value: embryonic

value: ENCBS588KBU at ENCODE; https://www.encodeproject.org/ENCBS588KBU/


title: Brain, Paxton benthic, female social control, trial 82

value: whole brain

value: Paxton benthic

value: female

value: female social control


title: Brain, Paxton benthic, heterospecific courtship, trial 77

value: heterospecific courtship


title: MPRA from HEK293 (ENCLB393OGC)

description:
https://www.encodeproject.org/experiments/ENCSR781PSG/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR781PSG
assay title: MPRA
assembly: hg19
possible controls: ENCSR701FXI
encode release date: 2021-09-10
lab: Ryan Tewhey, JAX
library encode accession: ENCLB393OGC
fragmentation methods: none

value: cell line

value: Ryan Tewhey, JAX

value: ENCBS245MLT at ENCODE; https://www.encodeproject.org/ENCBS245MLT/


title: Brain, Priest limnetic, female social control, trial 72

value: Priest limnetic


title: MPRA from HEK293 (ENCLB594WIS)

description:
https://www.encodeproject.org/experiments/ENCSR781PSG/
***************
biological replicate number: 5
technical replicate number: 1
description:
experiment encode accession: ENCSR781PSG
assay title: MPRA
assembly: hg19
possible controls: ENCSR701FXI
encode release date: 2021-09-10
lab: Ryan Tewhey, JAX
library encode accession: ENCLB594WIS
fragmentation methods: none

value: not applicable

value: ENCBS337JLA at ENCODE; https://www.encodeproject.org/ENCBS337JLA/


title: MPRA from GM12878 (ENCLB515OAJ)

description:
https://www.encodeproject.org/experiments/ENCSR812PWW/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR812PWW
assay title: MPRA
assembly: hg19
possible controls: ENCSR720LEA
encode release date: 2021-09-10
lab: Ryan Tewhey, JAX
library encode accession: ENCLB515OAJ
fragmentation methods: none

value: adult

value: ENCBS064RJT at ENCODE; https://www.encodeproject.org/ENCBS064RJT/


title: Brain, Paxton benthic, female social control, trial 89


title: Brain, Priest limnetic, heterospecific courtship, trial 71


title: Brain, Paxton limnetic, heterospecific courtship, trial 70

value: Paxton limnetic


title: MPRA from HEK293 (ENCLB094ZVA)

description:
https://www.encodeproject.org/experiments/ENCSR781PSG/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR781PSG
assay title: MPRA
assembly: hg19
possible controls: ENCSR701FXI
encode release date: 2021-09-10
lab: Ryan Tewhey, JAX
library encode accession: ENCLB094ZVA
fragmentation methods: none

value: unknown

value: ATCC

value: ENCBS285BNN at ENCODE; https://www.encodeproject.org/ENCBS285BNN/


title: MPRA from HEK293 (ENCLB867BEC)

description:
https://www.encodeproject.org/experiments/ENCSR781PSG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR781PSG
assay title: MPRA
assembly: hg19
possible controls: ENCSR701FXI
encode release date: 2021-09-10
lab: Ryan Tewhey, JAX
library encode accession: ENCLB867BEC
fragmentation methods: none

value: embryonic

value: ENCBS394ZMF at ENCODE; https://www.encodeproject.org/ENCBS394ZMF/


title: Brain, Priest limnetic, conspecific courtship, trial 68

value: whole brain

value: female

value: conspecific courtship


title: MPRA from SK-N-SH (ENCLB109ZTA)

description:
https://www.encodeproject.org/experiments/ENCSR742AAP/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR742AAP
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB109ZTA
fragmentation methods: none

value: SK-N-SH

value: cell line

value: Metastatic neuroblastoma from bone marrow

value: child

value: 4 years

value: ENCBS562CND at ENCODE; https://www.encodeproject.org/ENCBS562CND/


title: Brain, Paxton benthic, conspecific courtship, trial 67

value: Paxton benthic


title: Brain, Paxton benthic, female social control, trial 87

value: female social control


title: MPRA from SK-N-SH (ENCLB540HTX)

description:
https://www.encodeproject.org/experiments/ENCSR742AAP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR742AAP
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB540HTX
fragmentation methods: none

value: not applicable

value: Ryan Tewhey, JAX

value: ENCBS550ITN at ENCODE; https://www.encodeproject.org/ENCBS550ITN/


title: Brain, Paxton benthic, conspecific courtship, trial 64


title: Brain, Paxton limnetic, female social control, trial 61

value: Paxton limnetic


title: Brain, Priest limnetic, heterospecific courtship, trial 59

value: Priest limnetic

value: heterospecific courtship


title: MPRA from SK-N-SH (ENCLB502MID)

description:
https://www.encodeproject.org/experiments/ENCSR742AAP/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR742AAP
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB502MID
fragmentation methods: none

value: ATCC

value: ENCBS429YRD at ENCODE; https://www.encodeproject.org/ENCBS429YRD/